


A Dark Ninja

by Toruhiiyi



Category: Sonic the Hedgehog (Video Games), Sonic the Hedgehog - All Media Types
Genre: Angst with a Happy Ending, Brainwashing, Fights, Gen, Gift Fic, Not Beta Read, Out of Character
Language: English
Status: Completed
Published: 2020-03-30
Updated: 2020-03-30
Packaged: 2021-02-28 18:14:09
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 1
Words: 3,511
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/23401303
Author URL: https://archiveofourown.org/users/Toruhiiyi/pseuds/Toruhiiyi
Summary: Gift for: @bungledungle on twitter, based around her evil Sonic designShadow is rushing through the city, when he sees something different than anything he's ever experienced. Sonic is standing there... but this time, standing with EggmanThree moments Shadow had to deal with an angry brainwashed Sonic
Relationships: Shadow the Hedgehog & Sonic the Hedgehog
Kudos: 18





	A Dark Ninja

Moment 1:  
With the blast of the jets from his hover shoes, Shadow sped across the fields in the night sky. The star drifted with him as he gracefully moved with swift precision. He got a call that Eggman robots were attacking the city, and asking him to take care of it. The whole restoration team has been excruciatingly busy as one day Sonic disappeared without reason. He said something about “clearing his mind” before taking off to Tails. That was a month ago. No one had seen him anywhere, and Amy was starting to get paranoid. So he’s been dealing with all the attacks Eggman started doing a week ago. 

Blasting into the city he saw the army of badniks reading their canons for the attack. Swiftly avoiding them and sliding through the dirt let a blast of dirt making the sensors go haywire. Then with a clean slash from his chaos spear, he split the badniks in half. A hammer was above him from a super badnik aiming his shot, but Shadow avoided swiftly with a grunt. He then ran up the hammer, to the badniks long arm, and stabbed the robots eye, hitting his internal processor. The badnik fell with an emotionless fall, making the dirt brush away from it, as Shadow stood up to analyse the situation. 

At the corner of his eye, he noticed some mobians hiding behind some rubble, gently walking over the frightened crowd, he saw that it seemed to be the bystanders at the time of the attack, he was happy there were no casualties. 

“Is anyone hurt?” He called at the group, getting straight to the point.

A young mother spoke up, as she cradled her child, “No sir!”

“Good, keep moving past that street.” He said as he pointed to the way he came. “I came from that direction, so you should be safe. There's a resistance truck at the end, for your escape.” He said as the group started running. He started moving forward to get the remaining enemies, not aware of the figure looking on in the shadows. 

“This fool can move like me… how pathetic.”

Shadow kept moving and destroyed badniks, clearing the path. He stopped to take a breather as he didn’t see anything move by. He then heard a click and turned around to see a smoke bomb already releasing the smoke. He started coughing, as he was trying to see through.

Then with a swift kick, a black figure appeared from the smoke and sent him into a wall. Just as Shadow started to stand up as the bricks fell off him, the figure appeared again from nowhere and roundhouse kicked him into the road. 

“Pathetic, you're the ultimate hotshot and you can’t avoid two kicks?” The figure spoke. 

Shadow stood up from the ground, grunting at the pain. Who the hell was this guy to be able to attack like that?  
“Big talk for-”

The figure appeared out of nowhere and kicked Shadow in the head.

“Pay attention will ya? I hate boring speeches.” 

This time, Shadow was prepared, he reached his hand and grabbed the scarf the figure was accompanied by. Spinning him around to the ground, the scarf was lifted down from his chin.

“That's…” Shadow said, stricken with shock as the figure all along, was the missing Sonic the hedgehog. 

Sonic jumped up and moved away from Shadow, with anger in his eyes.

“How the hell do you know my name.”

“Sonic… what… what happened to you?”

“That doesn’t answer my question.”

“Oh HO HO HO!” A recurring laugh coming from Eggman appeared, flying down from his egg mobile to the two. 

“Eggman… What are you doing here?!” Shadow questioned. 

“Master… who the hell is this faker.” Sonic questioned himself. Sonic referring to his mortal enemy as “master” put a pit in Shadow's stomach, it felt so unnatural. 

“This fool works for those losers in the resistance, obviously no match for you. I’ve already taken the chaos emeralds from this area. Properly deal with him.”

“You're giving me too much fun.” Sonic responded, rushing in to attack him.

Shadow had barely any time to anticipate the attack, blocking the attack, but it was futile as Sonic punched Shadow in his unguarded stomach, sending him in the air. Sonic then jumped above sending him crashing down into the floor as the ground broke under him sending rubble everywhere. 

“Hmph, pathetic.” Sonic said as he drifted back into the smoke created by the rubble and disappeared. 

Shadow looked on in shock, rushing around just to find Sonic. But he came up with no results. Why was Sonic working for Eggman? It didn’t make any sense! Also this time Sonic was more powerful than usual, he was fighting harsher. Did that mean? Shadow suddenly realized something, the reason Sonic was stronger was because this time he wasn’t holding his power back.

Moment 2:

Eggman was flipping through his cameras analyzing the resistance moves, as they were starting to recover him. They already have tried to get Sonics memory back by just talking to him, trying to get him to remember why he fought. This wasn't a concern. The drive that was inserted into Sonic made it clear that his memory would never return. To undo his adjustments, the chip would have to be gone from the inside, as a forced removal would equate to death. 

“If you're just going to waste your time, I’ll be in my room.” Sonic said, moving away. Cubot slowly followed him, noticing something off about Sonic. He could see Sonic didn’t have a smug expression under his mask. The current one was frowning, filled with contempt. 

Sonic walked down the hallway, with his feet moving more harsher than usual. He looked down, his scarf covering more of his face than usual. He looked on in deep questioning, like something was on his mind. 

“What the hell was that faker on about?” He asked, remembering the previous fight.

…

Sonic was on top of a roof, analyzing the busy streets of mobius in the glistening moonlight. He felt like no one could see him in the shadows, like he was safe. He wanted no one to hurt him, anyone who brought pain to him would pain.

“What are you even doing?” A familiar darker voice came from below, behind he was facing. Turning around, he saw Shadow looking up at him from the ground opposite to him looking. Shadow’s eyes were different from their first encounter, as instead of confusion, the glistened with anger. He clearly had a different mentality this time, filled with knowledge and preparation. 

“I have a lot of questions for you, Sonic!” Shadow sternly said from below, as Sonic turned around to him. Sonic jumped down and pulled out a few kunai knives shaped as rings, he threw at Shadow, as he moved away from the onslat. Sonic dash ahead, but Shadow moved close to him as well, as they started fist fighting. They grasped each other's hands from punching, trying to push into each other. 

“Why the hell are you siding with Eggman?!” Shadow yelled through this standoff.

“I need to protect myself! Everyone in this universe would hurt me!” 

Sonic pushed Shadow away with this statement, as Shadow jumped and landed  
on his feet.

“You don’t believe that for a second.” Shadow replied with full seriousness.  
“How dare you!” Sonic yelled, spindashing all over the place, using the walls as leverage to boost off of. 

Shadow used this opportunity while avoiding them to talk to Sonic. “Remember your friends! Remember your home! Remember all the people you helped! Remember who you are!” Shadow avoided them, grasping Sonic in one, and throwing him away, ignoring the blood coming off his hands from Sonic’s quills. Sonic came out of the ball and landed on the floor. 

“What the hell are you talking about! I have no one!” Sonic yelled, not realizing Shadow running up to him, able to get an uppercut in Sonic’s stomach. The air came out of Sonics lungs, and he fell up in the air and back down on the floor. 

Sonic started breathing frantically when he sat up. His eyes started shaking frantically, clearly panicked over the situation. The world to Sonic started to blur, he felt like he was going to die. He felt like a memory was gone… like he was missing something… “You hurt me…” Sonic started to say to himself. Sonic then got up and yelled a war cry. He pointed to Shadow with anger boiling in his eyes. “You hurt me! People like you are evil! I’ll fight back against all of you!” Sonic used the kunai blade to launch smoke across the battlefield, hindering Shadow vision. With the smoke Sonic used his time to launch a tirade of blades to Shadow, sending him back. He then mass punched Shadow, and launched all his energy into Shadows, chest, right where he hit him. That punch launched Shadow into a tree, hindering him unconscious. 

Sonic looked onward as the smoke cleared, walking up to Shadow drawing a blade in his land. He lifted up the blade, eyeing Shadow below him. For some reason, Sonic stopped, he recused himself back into his scarf, drifting away into the smoke. 

…

Sonic laid in his room, which looked like a jail cell. His bed even looked like a prison bunk bed, which he was currently on. Orbot appeared through the door, causing Sonic to turn away from, unhappy of being seen. 

“You seem upset.” Orbot states, getting close to him.

“My condition should not bother you.” Sonic responded.

“I think some people would care for you.”

“Get real, I’m a weapon, I kill and get the job done.”

“Shadow was also a weapon.” Orbot responded, making Sonic flinch, clearly that piece of information getting to him. 

“Hmph, so that faker is more alike than I thought.”

“You clearly are the ultimate weapon.”

“Indeed I am, which is why that foolish hedgehog would never stop me, who does he think he is? Question me and who I am.”

“You're clearly questioning yourself.”

“What? No I’m not, I’ll destroy the world, I make all those fools pay for their treatment of me. People will learn to fear the name, Sonic.”

Moment 3:

Sonic made full promise on his threat of people remembering his name. He had taken over Eggman's entire operation, and now was on the space colony ark. Sonic was planning on destroying the world with the eclipse canon, as he gathered all the chaos emeralds to get it working. He would launch the attack in 5 minutes, as he stood on the balcony looking above. 

“Finally they will all pay… pay for the pain I feel.”

“Sonic stop! This isn’t you!” Shadow yelled, appearing behind Sonic on the balcony. 

“Ugh! Why will you never leave me alone!” Sonic yelled, frustrated at Shadow. 

“Because, you would never forgive yourself if you did this.”

“This again! What makes you think you know who I am?!”

“Because I was like you. I was so angry over what I suffered, I wanted closure. I didn’t know how to cope with the pain I felt deep in my heart. I had no clue on what I could do. I kept fighting against my feelings and emotions because I thought it was easier. I thought no one cared about me. But I know now that that's a big lie. People do care for me, and I’m holding my hand out to help you Sonic, just like you did for me.” Shadow said as he lifted his arm up to Sonic, leaving his hand open for him.

“This is a big trick! You’ll just cast me away! You’ll hate me because I’m a weapon! I caused so much destruction!” 

“That isn’t who you are Sonic, It's just how you feel. I promise I’ll fight how you feel with you, but you have to let me join you.” Shadow said, eyes glistening in determination.

Sonic looked on, clearly wanting to feel something, starting to give his hand to Shadow. But the chip inside Sonic shocked him, making him fall to the floor. He then got back up, looking sinister again. “As if I would join you! But since it's the end of the world… I’ll give you a taste of my power!” Sonic said, as then using the chaos emeralds to turn himself super. Using his super energy, he brought a mech suit into him. The suit had two giant arms that encased his arms, as then connected to the helmet brought on his head. The helmet has an orb brought in the back, Clearly for the chip to derive energy for. His legs obtained metal boots with lights going to the helmet as well. The helmet looked rather thin, only covering his eyes and the back of his head, the top and bottom of his head being open. Sonic looked on, his eyes encased with the two metal pieces connecting them, making an eye piece able to sense everything. The chaos emeralds making the armor also super, as the whole armor was graced with gold. 

“Bet you weren’t expecting my ultimate form! This form makes it so easy to kill you! Now die!” Sonic yelled, launching a strike at Shadow. Shadow flinched and closed his eyes, waiting for the attack. He felt upset, he couldn’t save Sonic just like he couldn’t save him. 

Shadow felt nothing, and he opened them to see him floating in water. He could somehow breathe in this. Looking around he could just see the sea for miles. “Did I die?” Shadow asked himself. 

“Not yet.” A feminine voice said, as gold particles flew to show Maria. 

“Maria.” Shadow said, as tears filled his eyes. Maria opened her arms, and Shadow rushed in to hug her.

“I- I M-m-mi-missed y-y-you so mu-m-much!” Shadow said through his crocodile tears, overwhelmed at seeing his friend again. 

“You’ve done so much good Shadow. I’m so proud of you.”

“But… If I’m not dead… then how are you here?”

“I am always with you. We are always with you.” More figures appeared with her, featuring Tikal, Chaos, Gerald, and more. “We're always watching and fighting along with you… so use the power you have with us. Us it to save Sonic.” Maria said, lifting her hand up to Shadow as she drifted away from the hug. Shadow smirked though this and grasped Marias hand, smiling.

Back on the arc, Sonic was smirking with his power. “How does that feel?! Ultimate lifeform?!” Sonic smugingly yelled as he stopped to power. As the smoke cleared, he was shocked to see Shadow was very much alive.

Shadow was protected by chaos barriers, with high chaos power Sonic could sense through his mask. Shadow appeared, not looking up, his eyes distilled on the floor. The chaos emeralds started glowing, as gold particles started appearing, swirling around Shadow. His quills started to sway with the movement of the particles, as Sonic’s mask dictated his power increasing. 

“What the heck? How is your power increasing? Impossible. What are you becoming?! I should have destroyed you. So how. How are you still standing? What are you doing?!”

Shadow looked up with full determination at this, and his body became super with light gold being part of his body. With this new form, he let a war cry. 

“It’s called… SUPER SHADOW!”

Shadow removed his inhibitor rings, he knew he only had one shot at this. The eclipse cannon would release its power in 3 minutes, and couldn’t be done on his own. But with the removal, he only had 3 minutes to save Sonic, if he exceeded the 3 minute timer, Shadow would die.

He chaos controlled into space to get Sonic out in the open, and Sonic took the bait in this form. Sonic also chaos controlled out and punched forward to Shadow, able to get a hit, sending Shadow flying.

‘Damn it, he’s faster than me.’ Shadow thought as he stopped and flew towards Sonic. ‘If I lose here… that means I will.. Die? No that won't happen. I refuse to die here!” Shadow chaos controlled right behind Sonic and kicked him in the head. Sonic grasped the foot above, preventing it from moving. Shadow could see the orb moving around like an eye, clearly that was affecting Sonic's ability to not remember. Sonic swung Shadow forward and used the glove to launch missiles into Shadow.

Shadow quickly noticed and swiftly avoided every one and punched Sonic in the face, but Sonic used his mecha legs to kick Shadow away, sending him a great distance. Shadow used this time to instead fly high and chaos spear him from above. Sonic flew straight towards him and maneuvered away from every attack. Shadow and Sonic kept mass punching each other, so shadow launched a chaos blast to remove Sonic away from him. Shadow's blood felt like it was burning, the pain was intense. But he had to keep fighting. If he failed, both Sonic and the world would die.

Shadow and Sonic kept flying into each other, each time being confronted with an attack, sending them back a few kilometers, but then flying back to where they were. Every swift punch and kick was deflected by the opposing person.

Shadow had reached his 30 seconds left, and his vision started to become blurry. His arm started melting, as the chaos energy was burning him alive. Shadow realizing he had no option further, he rushed towards Sonic. Sonic launched his chaos spears in retaliation, but Shadow was faster this time. He rushed and grabbed Sonic in an enticing hold and pushed him. Sonic struggled at this, wanting to let go, but Shadow's hold was too tight.  
“Let me go, damn it!” Sonic yelled as he couldn’t get away.

“No!” Shadow retorted louder at him. “I’m not letting you go until you're back to normal!” 

Shadow moved faster into the direct impact of the eclipse canon. “You're covered in metal and junk I know the real you would hate!” Shadow yelled as the countdown was 5 seconds until impact. “So you're going to take it all off!” Shadow yelled as he ran into the eclipse cannon, causing him and Sonic to take the whole blast. The power got the mech suit obliterated and his eggman brainwashed gear, as the chip erased in the blast. The canon power hit a target, and therefore stopped, not hitting the earth.

Shadow and Sonic were both falling unconsciously into the earth. Luckily, a two tailed fox had brought a spaceship to pick the two up and repair them. The recovery process was difficult. Sonic had remained fine under the blast, but Shadow was in serious condition. They both were taken to the medical ward of the resistance. Rouge had cuffs on Tails' ship for Shadow, causing him to regenerate slowly, he was lucky his heart somehow survived, as if it also got destroyed in the blast, Shadow would be permanently dead. 

Sonic remained unconscious for a week at this point. Shadow was better and working on missions, he had returned to the base, and went to check on sonics vitals. He arrived as the door opened with a swish, and he noticed Sonic was awake this time, sitting in his hospital bed, but facing away from Shadow.

“Sonic-” Shadow started but was quickly interrupted.

“What are you doing here?!” Sonic yelled, turning around, his eyes glistening with fear. 

“I came to check on you.” Shadow calmly stated despite Sonics clear paranoia.

“I’m a horrible person, you shouldn’t.” Sonic said as he looked down on his lap, avoiding giving eye contact from Shadow.

“Sonic you were brainwashed by eggman.”

“So?” Sonic said in a defeated tone.

“Sonic, you can’t blame yourself for doing something against your will.”

“How?!” Sonic looked up at Shadow this time. “I keep doing things that hurt others. How can I be a hero if all I do is hurt people?!” 

“Sonic, you are a hero, because you keep saving people no matter what the odds are. It doesn’t matter how much pain a person is going through, because you always rush to save them. You still tried to save me when I attacked the earth, and that's why I did the same for you. It doesn’t matter who thinks you're not a hero, because your actions make up for that.”

Sonic eyes stopped shaking in paranoia, they instead looked… relieved. Sonic sighed at this, and looked up with his trademark smirk. “Thanks Shads, I really needed that peep talk.”

“Hmph, well don’t act like that again faker, there are plenty of people who care for you, and they are all waiting to see you recover.” Shadow said pointing to the door and grumpingly looking away.

“Oh my chaos! I forgot about Tails! Bye-Shads-Race-Ya-Soon!” Sonic yelled out as he ran away from the door to see his friends.

Shadow looked on and smirked to himself that Sonic was finally back.

**Author's Note:**

> There you have it! I hope you all enjoyed! Please comment your thoughts, as I love hearing everything you have to say.


End file.
